February 2012 - galaxy-dev - lists.galaxyproject.org

Galaxy Wiki
by John Major 01 Feb '12

01 Feb '12

Galaxy team- I've tried a few times to add some content to the FAQ, but the captcha questions keep failing, or i'm submitting the wrong answer. I'd suggest a slightly less burdensome barrier to contributing- i'm certain this is dialing down your user contributions significantly. John

4 3

Coverage for paired end data
by SHAUN WEBB 01 Feb '12

01 Feb '12

Hi all. I am analysing paired end chip-seq samples. With single end reads I have seen people extend reads by an inferred insert size and then create coverage files in wig format. I was wondering if there are any tools available for paired end data that will create a coverage file by looking at properly mapped paired ends in a bam file and extending coverage across the distance between them. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

Error executing tool: 'fasta'
by Liisa Koski 01 Feb '12

01 Feb '12

Hi, I have tried running (on my local instance) a number of tools (fasta_to_tabular, tandem_repeat_finder, others) on my fasta file but keep getting the error Error executing tool: 'fasta' after file execution. In the log file I see this 10.1.1.119 - - [27/Jan/2012:15:47:15 -0400] "GET /tool_runner?tool_id=fasta2tab HTTP/1.1" 200 - " http://domain:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; WOW64; rv:6.0) Gecko/20100101 Firefox/6.0" galaxy.tools ERROR 2012-01-27 15:47:17,647 Exception caught while attempting tool execution: Traceback (most recent call last): File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1184, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1503, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 199, in execute build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) KeyError: 'fasta' The fasta file is ok because I have a development installation and the tools work fine there. So there is something wrong with my production installation. I did a diff between the files galaxy_dist/lib/galaxy/tools/__init__.py and lib/galaxy/tools/actions/__init__.py but they are the same. Any help would be much appreciated. Thanks, Liisa

2 1

Moving Galaxy's installed folder
by Peter Cock 01 Feb '12

01 Feb '12

Hi all, Is there any official guidance on relocating a working Galaxy installation? Ours is currently up and running using PostreSQL, with everything installed under /opt/galaxy-dist I want to move this under /mnt/galaxy (a RAID partition which will be shared with a cluster). What needs to be done to make this move? In particular, I am worried there may be some absolute paths in the database which would need updating. In principle if only relative paths are used, everything will be fine... Any advice? Thanks, Peter

2 6

Uploading metadata with file using Web API
by Oren Livne 01 Feb '12

01 Feb '12

Dear All, I have a file path that I'd like to link into Galaxy using a RESTful WEB API call with some additional metadata key-value pairs. How can I do that? I know the /api/libraries/ call respects JSON keys like "folder_id", "file_type", etc. But can I pass to it additional keys and it will know to store them with the file entry? Thank you so much, Oren

2 1

Problems with DataImport
by Ted Goldstein 01 Feb '12

01 Feb '12

Hi there, Here are three interrelated issues. I am trying to use Galaxy with some large cancer genomic datasets here at UCSC and do some systems biology. I have petabyte size dataset data libraries which will constantly be in flux at the edges. I would prefer to just have the Galaxy read the metadata from the file system for large datasets without using the database. Is there a convenient api boundary to write an adapter to the dataset object interface? In the meantime, I am going to try to just import day using the link. Its great that this feature is in already When I import into a couple of a modest megabyte size dataset using "Link to files without copying to Galaxy" option, the status never changes from "queued". Is this a bug? Is there a known work around? I have many large datasets. Also, it takes a long time to expand the dataset name link. (My experiment on import is a data tree of about a thousand files). Is this a known bug? Thanks! Ted

2 2

Re: [galaxy-dev] Unix user account/connection and Galaxy connection
by Ann Black 01 Feb '12

01 Feb '12

Hi all - I am working on transitioning our test galaxy -> production and this is how I have decided to handle unix & galaxy users. I have two groups created on our cluster. 1) galaxyadmin and 2) galaxyusers. galaxyadmin is a subset of galaxyusers. We have authentication occurring in an apache front to our campus id/passwd. I then place the campus id as well as campus email in the request header during the proxy to galaxy. The email is used as the galaxy id. I have augmented galaxy code such that when a new user logs onto galaxy and galaxy auto-creates the galaxy account, it also kicks off scripts that configure the unix account. It creates a new unix account if it does not exist (group galaxyusers), otherwise will augment the existing user's default group (keeping all other group relationships) to be galaxyusers. I have installed the latest version of openSSH. I have prevented all galaxyusers from sshing into the box, and instead set up a sftp jail. The sftp jail directory is not the user's home directory. The sshd_config also allows me to specify a sftp umask, so when a user puts a file into their sftp jail, it will be readable/writeable to anyone in the galaxyusers group (note the jail and preventing ssh does not expose the files to any other users). As part of the scripts that get kicked off in galaxy to create/mod a user - I also create the necessary ftp links to galaxy. I create a symlink from galaxy's ftp directory with the galaxy user id (email) to the user's jailed sftp directory (username). This allows galaxy runtime to import without problems since the files are galaxyusers group read/writeable. My galaxy runs under a galaxy userid (not root) but I have augmented the sudoers file to allow for just that id to have access to specific commands in order to adjust useraccounts. This has been all working in our production prototype testing and we will be having a security review on it shortly - but it should be sound. Hope this helps! > >Message: 11 >Date: Mon, 30 Jan 2012 09:31:15 -0500 >From: David Hoover <hooverdm(a)helix.nih.gov> >To: Sarah Maman <sarah.maman(a)toulouse.inra.fr> >Cc: galaxy-dev(a)lists.bx.psu.edu >Subject: Re: [galaxy-dev] Unix user account/connection and Galaxy > connection >Message-ID: <A0EE343C-C9F5-4039-B684-DD370FB2FDA4(a)helix.nih.gov> >Content-Type: text/plain; charset="us-ascii" > >I'd love to know answers to this question as well. So far, all I've done >is create two tools for copying files between Galaxy and a user's >personal directories using a rather dangerous setuid executable. > >I have mulled over two possibilities for this problem. One is to run >Galaxy as root. The other is for each user to kick off their own >personal instance of Galaxy as themselves, but accessing the same main >database and file repository. The latter would require all files be >read-write accesible to all users. Neither is good. > >On Jan 30, 2012, at 4:29 AM, Sarah Maman wrote: > >> Dear all, >> >> There is currently no link between an user ssh connection on his own >>account (own space on Unix) and the Galaxy connection. >> How to run Galaxy on an Unix user account? How to link the data storage >>system and the Unix user account (symlink?)? >> >> The goal is to not need to copy or move data. >> >> >> PS : Thanks a lot to David, Gordon, Brad, Christophe and Nate for your >>help on LDAP authentification. >> I always try to find a solution (Apache configuration). I will inform >>Galaxy list when I will find a solution. >> >> >> Thanks in advance, >> >> Sarah > > > > > >******************************************

1 1

Missing eggs for DRMMA?
by Peter Cock 01 Feb '12

01 Feb '12

Hi all, I'm working on a test setup using an SGE cluster. During start of run.sh up I see: galaxy.jobs ERROR 2012-02-01 15:03:14,164 Job runner is not loadable: galaxy.jobs.runners.drmma Traceback (most recent call last): File "/data/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 1187, in _load_plugin module = __import__( module_name ) ImportError: No module named drmma According to this wiki page, Galaxy provides the DRMMA egg: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster However, Galaxy is not downloading a DRMAA egg, in fact there are none here: http://eggs.g2.bx.psu.edu/DRMAA_python/ Is this a documentation problem? Or a just missing egg? Should I scramble it myself locally? Thanks, Peter

2 3

Re: [galaxy-dev] Error viewing BAM files in IGV
by Nate Coraor 01 Feb '12

01 Feb '12

On Jan 17, 2012, at 10:50 AM, Alexander Graf wrote: > Hi Nate, > sorry for my late reply, but I was on holiday last weeks. > I have looked in my apache error.log and access.log resulting into no new insights - no output is given there. > So I gave nginx a try, getting the same error as before. > I think it is not a configuration issue of apache or nginx, but I don't have any clue any more what's going on. > Hope you or somebody else can help me figure out the problem. Hi Alex, I thought this might be a problem with the way Galaxy was handling proxy prefixes (/galaxy) but I don't believe that's the problem. It looks like your XSendFile config is not working, as evidenced by the 'HEAD' HTTP commands in the Galaxy log (these should be interrupted by the Apache/nginx server and not passed through to Galaxy). Check your proxy server logs. --nate > > Alex > > Below are the newly generated error logs: > > > If I try to view the BAM file locally, I get: > > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/local_default HTTP/1.0" 302 - "http://10.153.182.203/galaxy/history" "Mozilla/5.0 (Ubuntu; X11; Linux x86_64; rv:9.0.1) Gecko/20100101 Firefox/9.0.1" > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/local_default/5ce1ba9f488a6ce5/data/galaxy_8b4e4b7bbaf9bc68.bam.bai HTTP/1.0" 302 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM Java/1.6.0_22" > galaxy.web.framework DEBUG 2012-01-17 16:34:25,389 Error: this request returned None from get_history(): http://10.153.182.203/galaxy/root > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET /galaxy/root?app_action=data&user_id=5ce1ba9f488a6ce5&app_name=igv_bam&link_name=local_default&action_param=galaxy_8b4e4b7bbaf9bc68.bam.bai&dataset_id=8b4e4b7bbaf9bc68 HTTP/1.0" 200 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM Java/1.6.0_22" > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "HEAD /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/local_default/5ce1ba9f488a6ce5/data/galaxy_8b4e4b7bbaf9bc68.bam HTTP/1.0" 302 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM Java/1.6.0_22" > galaxy.web.framework DEBUG 2012-01-17 16:34:25,470 Error: this request returned None from get_history(): http://10.153.182.203/galaxy/root > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "HEAD /galaxy/root?app_action=data&user_id=5ce1ba9f488a6ce5&app_name=igv_bam&link_name=local_default&action_param=galaxy_8b4e4b7bbaf9bc68.bam&dataset_id=8b4e4b7bbaf9bc68 HTTP/1.0" 200 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM Java/1.6.0_22" > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/local_default/5ce1ba9f488a6ce5/data/galaxy_8b4e4b7bbaf9bc68.bam HTTP/1.0" 302 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM Java/1.6.0_22" > galaxy.web.framework DEBUG 2012-01-17 16:34:25,639 Error: this request returned None from get_history(): http://10.153.182.203/galaxy/root > XX.XXX.XXX.XXX - - [17/Jan/2012:16:34:25 +0200] "GET /galaxy/root?app_action=data&user_id=5ce1ba9f488a6ce5&app_name=igv_bam&link_name=local_default&action_param=galaxy_8b4e4b7bbaf9bc68.bam&dataset_id=8b4e4b7bbaf9bc68 HTTP/1.0" 200 - "-" "IGV Version 2.0.34 (1623)01/14/2012 12:45 AM Java/1.6.0_22" > > > and if I run it with the web current, I still get: > > galaxy.web.framework DEBUG 2012-01-17 16:35:26,820 Error: this request returned None from get_history(): http://10.153.182.203/galaxy/root > XX.XXX.XXX.XXX - - [17/Jan/2012:16:35:26 +0200] "HEAD /galaxy/root?app_action=data&user_id=5ce1ba9f488a6ce5&app_name=igv_bam&link_name=web_link_main&action_param=galaxy_8b4e4b7bbaf9bc68.bam&dataset_id=8b4e4b7bbaf9bc68 HTTP/1.0" 200 - "-" "Java/1.6.0_22" > ---------------------------------------- > Exception happened during processing of request from ('127.0.0.1', 33901) > Traceback (most recent call last): > File "/opt/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread > self.finish_request(request, client_address) > File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request > self.RequestHandlerClass(request, client_address, self) > File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__ > self.finish() > File "/usr/lib/python2.6/SocketServer.py", line 661, in finish > self.wfile.flush() > File "/usr/lib/python2.6/socket.py", line 297, in flush > self._sock.sendall(buffer(data, write_offset, buffer_size)) > error: [Errno 32] Broken pipe > ---------------------------------------- > XX.XXX.XXX.XXX - - [17/Jan/2012:16:35:26 +0200] "GET /galaxy/display_application/8b4e4b7bbaf9bc68/igv_bam/web_link_main/5ce1ba9f488a6ce5/data/galaxy_8b4e4b7bbaf9bc68.bam HTTP/1.0" 302 - "-" "Java/1.6.0_22" > galaxy.web.framework DEBUG 2012-01-17 16:35:26,910 Error: this request returned None from get_history(): http://10.153.182.203/galaxy/root > > > > > 2011/12/19 Nate Coraor <nate(a)bx.psu.edu> > On Dec 14, 2011, at 4:22 PM, Alexander Graf wrote: > > > Hi nate, > > I have tried it with several BAM files, resulting in the same error. > > If I download the BAM and bai files from Galaxy and load it into IGV manually, everything works like charm. > > Up to now I could not figure out why it is not working. > > Could I have better success switching to the nginx-server? > > Hi Alex, > > It should work with Apache as well. I don't have an environment set up here to test, but could you take a look at the Apache access and error logs to determine whether the file is being found and read properly? It's possible that the request is returning something other than a 200 code and the file data. > > --nate > > > > > Alex > > > > Am 12.12.2011 um 16:11 schrieb Nate Coraor: > > > >> On Dec 9, 2011, at 6:45 AM, Alexander Graf wrote: > >> > >>> Hello, > >>> I have recently updated our Galaxy dist and I'm running into problems viewing BAM files in IGV (v2.0.22), saying: Invalid GZIP header. > >> > >> Hi Alex, > >> > >> Your config below looks okay at first glance. Can you verify that the file in question is a valid BAM? Or is this happening with all BAMs? > >> > >> --nate > >> > >>> I have configured the Apache as explained in the Wiki using this http.conf: > >>> > >>> > >>> ------------------------------------------------------------------------------------------------------------------------------------ > >>> <VirtualHost *:80> > >>> ServerName 127.0.0.1 > >>> RewriteEngine on > >>> > >>> RewriteRule ^/galaxy$ /galaxy/ [R] > >>> RewriteRule ^/galaxy/static/style/(.*) /opt/galaxy/static/june_2007_style/blue/$1 [L] > >>> RewriteRule ^/galaxy/static/scripts/(.*) /opt/galaxy/static/scripts/packed/$1 [L] > >>> RewriteRule ^/galaxy/static/(.*) /opt/galaxy/static/$1 [L] > >>> RewriteRule ^/galaxy/favicon.ico /opt/galaxy/static/favicon.ico [L] > >>> RewriteRule ^/galaxy/robots.txt /opt/galaxy/static/robots.txt [L] > >>> RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P] > >>> > >>> <Proxy http://localhost:8081> > >>> Order deny,allow > >>> Allow from all > >>> </Proxy> > >>> > >>> <Location "/galaxy"> > >>> # Define the authentication method > >>> XSendFile on > >>> XSendFilePath / > >>> # Compress all uncompressed content.http.conf > >>> SetOutputFilter DEFLATE > >>> SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary > >>> SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary > >>> </Location> > >>> <Directory "/galaxy/static"> > >>> ExpiresActive On > >>> ExpiresDefault "access plus 6 hours" > >>> </Directory> > >>> </VirtualHost> > >>> ---------------------------------------------------------------------------------------------------------------------------------------- > >>> > >>> > >>> By having this parts changed in universe_wsgi.ini: > >>> ---------------------------------------------------------------------------------------------------------------------------------------- > >>> [server:main] > >>> use = egg:Paste#http > >>> port = 8081 > >>> host = 0.0.0.0 > >>> use_threadpool = True > >>> > >>> [filter:gzip] > >>> use = egg:Paste#gzip > >>> > >>> [filter:proxy-prefix] > >>> use = egg:PasteDeploy#prefix > >>> prefix = /galaxy > >>> > >>> [app:main] > >>> paste.app_factory = galaxy.web.buildapp:app_factory > >>> filter-with = proxy-prefix > >>> cookie_path = /galaxy > >>> apache_xsendfile = True > >>> upstream_gzip = False > >>> ---------------------------------------------------------------------------------------------------------------------------------------- > >>> > >>> The resulting Galaxy error log is: > >>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > >>> galaxy.web.framework DEBUG 2011-12-09 12:32:08,825 Error: this request returned None from get_history(): http://10.153.182.203/galaxy/root > >>> 10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "GET /galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam.bai&dataset_id=9b0f702d0207cd78 HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM Java/1.6.0_22" > >>> 10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD /galaxy/display_application/9b0f702d0207cd78/igv_bam/local_default/c9a3f3a19e75965d/data/galaxy_9b0f702d0207cd78.bam HTTP/1.1" 302 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM Java/1.6.0_22" > >>> galaxy.web.framework DEBUG 2011-12-09 12:32:08,915 Error: this request returned None from get_history(): http://10.153.182.203/galaxy/root > >>> 10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD /galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam&dataset_id=9b0f702d0207cd78 HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM Java/1.6.0_22" > >>> ---------------------------------------- > >>> Exception happened during processing of request from ('127.0.0.1', 52683) > >>> Traceback (most recent call last): > >>> File "/opt/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread > >>> self.finish_request(request, client_address) > >>> File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request > >>> self.RequestHandlerClass(request, client_address, self) > >>> File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__ > >>> self.finish() > >>> File "/usr/lib/python2.6/SocketServer.py", line 661, in finish > >>> self.wfile.flush() > >>> File "/usr/lib/python2.6/socket.py", line 297, in flush > >>> self._sock.sendall(buffer(data, write_offset, buffer_size)) > >>> error: [Errno 32] Broken pipe > >>> ---------------------------------------- > >>> > >>> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > >>> > >>> > >>> Thanks in advance for your help > >>> > >>> Alex > >>> > >>> ___________________________________________________________ > >>> Please keep all replies on the list by using "reply all" > >>> in your mail client. To manage your subscriptions to this > >>> and other Galaxy lists, please use the interface at: > >>> > >>> http://lists.bx.psu.edu/ > > > > > > > > -- > ___________________________________________________________ > > Alexander Graf > > Laboratory of Functional Genome Analysis > Gene Center, University of Munich (LMU) > Feodor-Lynen-Strasse 25; 81377 Munich; Germany > email: graf(a)lmb.uni-muenchen.de > Internet: www.lafuga.de/genomics.htm > ___________________________________________________________ >

1 0

Re: [galaxy-dev] Error viewing BAM files in IGV
by Jim Johnson 01 Feb '12

01 Feb '12

Hi, I'm seeing the same behavior. Galaxy is returning a web page rather than the requested .bai index file for the BAM file. In class WebApplication ( lib/galaxy/web/framework/base.py ) in __call__( self, environ, start_response ) line 133 # Setup the transaction trans = self.transaction_factory( environ ) Gets routed to the root controller and returns the galaxy server main page html. JJ > On Dec 14, 2011, at 4:22 PM, Alexander Graf wrote: > >> Hi nate, >> I have tried it with several BAM files, resulting in the same error. >> If I download the BAM and bai files from Galaxy and load it into IGV manually, everything works like charm. >> Up to now I could not figure out why it is not working. >> Could I have better success switching to the nginx-server? > Hi Alex, > > It should work with Apache as well. I don't have an environment set up here to test, but could you take a look at the Apache access and error logs to determine whether the file is being found and read properly? It's possible that the request is returning something other than a 200 code and the file data. > > --nate > >> Alex >> >> Am 12.12.2011 um 16:11 schrieb Nate Coraor: >> >>> On Dec 9, 2011, at 6:45 AM, Alexander Graf wrote: >>> >>>> Hello, >>>> I have recently updated our Galaxy dist and I'm running into problems viewing BAM files in IGV (v2.0.22), saying: Invalid GZIP header. >>> Hi Alex, >>> >>> Your config below looks okay at first glance. Can you verify that the file in question is a valid BAM? Or is this happening with all BAMs? >>> >>> --nate >>> >>>> I have configured the Apache as explained in the Wiki using this http.conf: >>>> >>>> >>>> ------------------------------------------------------------------------------------------------------------------------------------ >>>> <VirtualHost *:80> >>>> ServerName 127.0.0.1 >>>> RewriteEngine on >>>> >>>> RewriteRule ^/galaxy$ /galaxy/ [R] >>>> RewriteRule ^/galaxy/static/style/(.*)/opt/galaxy/static/june_2007_style/blue/$1 [L] >>>> RewriteRule ^/galaxy/static/scripts/(.*)/opt/galaxy/static/scripts/packed/$1 [L] >>>> RewriteRule ^/galaxy/static/(.*)/opt/galaxy/static/$1 [L] >>>> RewriteRule ^/galaxy/favicon.ico /opt/galaxy/static/favicon.ico [L] >>>> RewriteRule ^/galaxy/robots.txt /opt/galaxy/static/robots.txt [L] >>>> RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P] >>>> >>>> <Proxyhttp://localhost:8081> >>>> Order deny,allow >>>> Allow from all >>>> </Proxy> >>>> >>>> <Location "/galaxy"> >>>> # Define the authentication method >>>> XSendFile on >>>> XSendFilePath / >>>> # Compress all uncompressed content.http.conf >>>> SetOutputFilter DEFLATE >>>> SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary >>>> SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary >>>> </Location> >>>> <Directory "/galaxy/static"> >>>> ExpiresActive On >>>> ExpiresDefault "access plus 6 hours" >>>> </Directory> >>>> </VirtualHost> >>>> ---------------------------------------------------------------------------------------------------------------------------------------- >>>> >>>> >>>> By having this parts changed in universe_wsgi.ini: >>>> ---------------------------------------------------------------------------------------------------------------------------------------- >>>> [server:main] >>>> use = egg:Paste#http >>>> port = 8081 >>>> host = 0.0.0.0 >>>> use_threadpool = True >>>> >>>> [filter:gzip] >>>> use = egg:Paste#gzip >>>> >>>> [filter:proxy-prefix] >>>> use = egg:PasteDeploy#prefix >>>> prefix = /galaxy >>>> >>>> [app:main] >>>> paste.app_factory = galaxy.web.buildapp:app_factory >>>> filter-with = proxy-prefix >>>> cookie_path = /galaxy >>>> apache_xsendfile = True >>>> upstream_gzip = False >>>> ---------------------------------------------------------------------------------------------------------------------------------------- >>>> >>>> The resulting Galaxy error log is: >>>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >>>> galaxy.web.framework DEBUG 2011-12-09 12:32:08,825 Error: this request returned None from get_history():http://10.153.182.203/galaxy/root >>>> 10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "GET /galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam.bai&dataset_id=9b0f702d0207cd78 HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM Java/1.6.0_22" >>>> 10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD /galaxy/display_application/9b0f702d0207cd78/igv_bam/local_default/c9a3f3a19e75965d/data/galaxy_9b0f702d0207cd78.bam HTTP/1.1" 302 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM Java/1.6.0_22" >>>> galaxy.web.framework DEBUG 2011-12-09 12:32:08,915 Error: this request returned None from get_history():http://10.153.182.203/galaxy/root >>>> 10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD /galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam&dataset_id=9b0f702d0207cd78 HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM Java/1.6.0_22" >>>> ---------------------------------------- >>>> Exception happened during processing of request from ('127.0.0.1', 52683) >>>> Traceback (most recent call last): >>>> File "/opt/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread >>>> self.finish_request(request, client_address) >>>> File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request >>>> self.RequestHandlerClass(request, client_address, self) >>>> File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__ >>>> self.finish() >>>> File "/usr/lib/python2.6/SocketServer.py", line 661, in finish >>>> self.wfile.flush() >>>> File "/usr/lib/python2.6/socket.py", line 297, in flush >>>> self._sock.sendall(buffer(data, write_offset, buffer_size)) >>>> error: [Errno 32] Broken pipe >>>> ---------------------------------------- >>>> >>>> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >>>> >>>> >>>> Thanks in advance for your help >>>> >>>> Alex >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> >>>> http://lists.bx.psu.edu/

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